Search results for: complete genome sequencing

Authors: Ronald Villamar-Torres, Michael Staudt, Christopher Viot

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Cotton Gossypium hirsutum L. is one of the most important industrial crops, producing the world leading natural textile fiber, but is very prone to arthropod attacks that reduce crop yield and quality. Cotton cultivation, therefore, makes an outstanding use of chemical pesticides. In reaction to herbivorous arthropods, cotton plants nevertheless show natural defense reactions, in particular through volatile organic compounds (VOCs) emissions. These natural defense mechanisms are nowadays underutilized but have a very high potential for cotton cultivation, and elucidating their genetic bases will help to improve their use. Simulating herbivory attacks by mechanical wounding of cotton plants in greenhouse, we studied by qPCR the changes in gene expression for genes of the terpenoids biosynthesis pathway. Differentially expressed genes corresponded to higher levels of the terpenoids biosynthesis pathway and not to enzymes synthesizing particular terpenoids. The genes were mapped on the G. hirsutum L. reference genome; their global relationships inside the general metabolic pathways and the biosynthesis of secondary metabolites were visualized with iPath2. The chromatographic profiles of VOCs emissions indicated first monoterpenes and sesquiterpenes emissions, dominantly four molecules known to be involved in plant reactions to arthropod attacks. As a result, the study permitted to identify potential key genes for the emission of volatile terpenoids by cotton plants in reaction to an arthropod attack, opening possibilities for molecular-assisted cotton breeding in benefit of smallholder cotton growers.

Keywords: biosynthesis pathways, cotton, mechanisms of plant defense, terpenoids, volatile organic compounds

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Authors: Kidane workelul, Li xu, Xiaoyang Pang, Jiaping Lv

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Dairy products are exceptionally ideal media for the growth of microorganisms because of their high nutritional content. There are several ways that milk might get contaminated throughout the milking process, including how the raw milk is transported and stored, as well as how long it is kept before being processed. Psychrotrophic bacteria are among the one which can deteriorate the quality of milk mainly their heat resistance proteas and lipase enzyme. For this research purpose 8 selected strains of Psychrotrophic bacteria (Entrococcus hirae, Pseudomonas fluorescens, Pseudomonas azotoformans, Pseudomonas putida, Exiguobacterium indicum, Pseudomonas paralactice, Acinetobacter indicum, Serratia liquefacients)are chosen and try to determine their characteristics based on the research methodology protocol. Thus, the 8 selected strains are cultured, plated incubate, extracted their genomic DNA and genome DNA was amplified, the purpose of the study was to identify their Psychrotrophic properties, lipase hydrolysis positive test, their optimal incubation temperature, designed primer using the noble strain P,flourescens conserved region area in target with lipA gene, optimized primer specificity as well as sensitivity and PCR detection for lipase positive strains using the design primers. Based on the findings both the selected 8 strains isolated from stored raw milk are Psychrotrophic bacteria, 6 of the selected strains except the 2 strains are positive for lipase hydrolysis, their optimal temperature is 20 to 30 OC, the designed primer specificity is very accurate and amplifies for those strains only with lipase positive but could not amplify for the others. Thus, the result is promising and could help in detecting the Psychrotrophic bacteria producing heat resistance enzymes (lipase) at early stage before the milk is processed and this will safe production loss for the dairy industry.

Keywords: dairy industry, heat-resistant, lipA, milk, primer and psychrotrophic

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Authors: Indranil Bayal, Pradipta Panchadhyayee

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Path-spin hybrid entanglement generated and confined in a single spin-1/2 particle is converted to spin-spin hybrid interparticle entanglement, which finds its important applications in quantum information processing. This protocol uses beam splitter, spin flipper, spin measurement, classical channel, unitary transformations, etc., and requires no collective operation on the pair of particles whose spin variables share complete entanglement after the accomplishment of the protocol. The specialty of the protocol lies in the fact that the path-spin entanglement is transferred between spin degrees of freedom of two separate particles initially possessed by a single party.

Keywords: entanglement, path-spin entanglement, spin-spin entanglement, CNOT operation

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Authors: Fayiz Saifurahman, Noori Fida Mohammad

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Afghanistan produces the highest rate of wheat, it is the first source of food, and food security in Afghanistan is dependent on the availability of wheat. Although Afghanistan is the main producer of wheat, on the other hand, Afghanistan is the largest importers of flour. The objective of this study is to assess the structure and dynamics of the wheat market in Afghanistan, can compute with foreign markets, and increase the level of production. To complete this, a broad series of secondary data was complied with, group discussions and interviews with farmers, agricultural and market experts. The research findings propose that; the government should adopt different policies to support the local market. The government should distribute the seed, support financially and technically to increase wheat production.

Keywords: Afghanistan, wheat, production , import

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Authors: Jiankang Wang, Hongyang Yu

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This paper proposes a portable online 3D modeling method. The method first utilizes a depth camera to collect data and compresses the depth data using a frame-by-frame lossless data compression method. The color image is encoded using the H.264 encoding format. After the cloud obtains the color image and depth image, a 3D modeling method based on bundlefusion is used to complete the 3D modeling. The results of this study indicate that this method has the characteristics of portability, online, and high efficiency and has a wide range of application prospects.

Keywords: 3D reconstruction, bundlefusion, lossless compression, depth image

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Authors: Rawaa Maher, Ahmed Allam, Haruichi Kanaya, Adel B. Abdelrahman

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In this paper, a compact, high-efficiency integrated rectenna is presented to operate in the 2.45 GHz band. A comparison between two rectifier topologies is performed to verify the benefits of removing the matching network from the rectifier. A rectifier high conversion efficiency of 74.1% is achieved. To complete the rectenna system, a novel omnidirectional antenna with high gain (3.72 dB) and compact size (25 mm * 29 mm) is designed and fabricated. The same antenna is used with a reflector for raising the gain to nearly 8.3 dB. The simulation and measurement results of the antenna are in good agreement.

Keywords: internet of things, integrated rectenna, rectenna, RF energy harvesting, wireless sensor networks(WSN)

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Authors: Kehinde Augustina Odukoya

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This study examines the portrayal of women in Nigerian magazine advertisements, with the aim to investigate whether there is sexualization of women in the advertisements. To achieve this aim, content analyses of 61 magazine advertisements from 5 different categories of magazines; a general interest magazine (Genevieve), fashion magazine (Hints Complete Fashion), men’s magazine (Mode), women’s magazine (Totally Whole) and a relationship magazine (Forever) were carried out. Erving Goffman’s 1979 frame analysis and Kang’s two additional coding categories were used to investigate the sexualization of women. Findings show that women are used for decorative purposes and objectified in over 70 per cent of the advertisements analyzed. Also, there is sexualization of women in magazine advertisements because women are nude 57.4 percent of the magazine advertisements.

Keywords: advertisements, magazine, sexualization, women

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Authors: Edwin Calderon-Mendoza, Patrick Schweitzer, Serge Weber

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Series arc faults appear frequently and unpredictably in low voltage distribution systems. Many methods have been developed to detect this type of faults and commercial protection systems such AFCI (arc fault circuit interrupter) have been used successfully in electrical networks to prevent damage and catastrophic incidents like fires. However, these devices do not allow series arc faults to be located on the line in operating mode. This paper presents a location algorithm for series arc fault in a low-voltage indoor power line in an AC 230 V-50Hz home network. The method is validated through simulations using the MATLAB software. The fault location method uses electrical parameters (resistance, inductance, capacitance, and conductance) of a 49 m indoor power line. The mathematical model of a series arc fault is based on the analysis of the V-I characteristics of the arc and consists basically of two antiparallel diodes and DC voltage sources. In a first step, the arc fault model is inserted at some different positions across the line which is modeled using lumped parameters. At both ends of the line, currents and voltages are recorded for each arc fault generation at different distances. In the second step, a fault map trace is created by using signature coefficients obtained from Kirchhoff equations which allow a virtual decoupling of the line’s mutual capacitance. Each signature coefficient obtained from the subtraction of estimated currents is calculated taking into account the Discrete Fast Fourier Transform of currents and voltages and also the fault distance value. These parameters are then substituted into Kirchhoff equations. In a third step, the same procedure described previously to calculate signature coefficients is employed but this time by considering hypothetical fault distances where the fault can appear. In this step the fault distance is unknown. The iterative calculus from Kirchhoff equations considering stepped variations of the fault distance entails the obtaining of a curve with a linear trend. Finally, the fault distance location is estimated at the intersection of two curves obtained in steps 2 and 3. The series arc fault model is validated by comparing current registered from simulation with real recorded currents. The model of the complete circuit is obtained for a 49m line with a resistive load. Also, 11 different arc fault positions are considered for the map trace generation. By carrying out the complete simulation, the performance of the method and the perspectives of the work will be presented.

Keywords: indoor power line, fault location, fault map trace, series arc fault

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Authors: K. Genise, S. Murthy

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Introductory Statement: The results of this retrospective chart review suggest the effects of bacterial colonization in critically ill children with viral bronchiolitis, currently unproven, are clinically insignificant. Background: Viral bronchiolitis is one of the most prevalent causes of illness requiring hospitalization among children worldwide and one of the most common reasons for admission to pediatric intensive care. It has been hypothesized that co-infection with bacteria results in more severe clinical outcomes. Conversely, the effects of bacterial colonization in critically ill patients with bronchiolitis are poorly defined. Current clinical management of colonized patients consists primarily of supportive therapies with the role of antibiotics remaining controversial. Methods: A retrospective review of all critically ill children admitted to the BC Children’s Hospital Pediatric Intensive Care Unit (PICU) from 2014-2017 with a diagnosis of bronchiolitis was performed. Routine testing in this time frame consisted of complete pathogen testing, including PCR for Streptococcus pneumoniae. Analyses were performed to determine the impact of bacterial colonization and antibiotic use on a primary outcome of PICU length-of-stay, with secondary outcomes of hospital length-of-stay and duration of ventilation. Results: There were 92 patients with complete pathogen testing performed during the assessed timeframe. A comparison between children with detected Streptococcus pneumoniae (n=22) and those without (n=70) revealed no significant (p=0.20) differences in severity of illness on presentation as per Pediatric Risk of Mortality III scores (mean=3.0). Patients colonized with S. pneumoniae had significantly shorter PICU stays (p=0.002), hospital stays (p=0.0001) and duration of non-invasive ventilation (p=0.002). Multivariate analyses revealed that these effects on length of PICU stay and duration of ventilation do not persist after controlling for antibiotic use, presence of radiographic consolidation, age, and severity of illness (p=0.15, p=0.32). The relationship between colonization and duration of hospital stay persists after controlling for these variables (p=0.008). Conclusions: Children with viral bronchiolitis colonized with S. pneumoniae do not appear to have significantly different PICU length-of-stays or duration of ventilation compared to children who are not colonized. Colonized children appear to have shorter hospital stays. The results of this study suggest bacterial colonization is not associated with increased severity of presenting illness or negative clinical outcomes.

Keywords: bronchiolitis, colonization, critical care, pediatrics, pneumococcal, infection

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Authors: Loubna Safar, Lama Youssef, Majd Aljamali

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Age-related macular degeneration (AMD) is one of the leading causes of blindness worldwide. Complement factor H polymorphism (Y402H) is thought to play a potential role in the predisposition to AMD and response of patients with exudative AMD to treatment with anti-Vascular Endothelial Growth Factor (anti-VEGF). This study aimed to investigate the frequency of Y402H among Syrians, its impact on their susceptibility to AMD, and the hypothesized role of Y402H in patients' response to intravitreal anti-VEGF (i.e.,, bevacizumab). Our case-control study encompassed unrelated 54 AMD cases and 44 controls. Genotyping was determined by standard sequencing of PCR products. Frequency was compared between patients and controls, and correlation between genotype and response to treatment was assessed in 20 patients with wet AMD who received a therapeutic course of three intravitreal bevacizumab injections (once monthly). Our results revealed a significantly higher prevalence of the risk allele C among AMD cases (51.9%) in comparison with controls (37.5%) (P= 0.04, OR= 1.386, CI= 0.999- 1.923). Patients with the TT genotype (no risk allele) exhibited a significantly better primary response rate, reached 87.5% compared to only 41.7% in patients carrying the risk allele C (TC + CC), (P= 0.04, OR= 9.8, CI=0.899- 106.84). The findings of this study prove the importance of investigating Y402H polymorphism as a prognostic marker for predicting response to bevacizumab in AMD patients.

Keywords: age-related macular degeneration, bevacizumab, complement factor H gene, polymorphism, Y402H

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Authors: Arpit Gite

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Purpose: We have evaluated the role of Total Neoadjuvant Therapy in patients with Locally Advanced Rectal cancer by giving Chemoradiotherapy followed by consolidation chemotherapy (CRT-CNCT) and, after that, the strategy of wait and watch. Methods: In this prospective case series, we evaluated the results of three locally advanced Rectal cancers, two cases Stage II (cT3N0) and one case Stage III ( cT4aN2). All three patients' growth was 4-6 cm from the anal verge. We have treated with Chemoradiotherapy to dose of 45Gy/25 Fractions to elective nodal regions (Inguinal node in anal canal Involvement)and Primary and mesorectum (Phase I) followed by 14.4Gy/8 Fractions to Primary and Mesorectum(Phase II) to a total dose of 59.4Gy/33 Fractions with concurrent chemotherapy Tab Capecitabine 825mg/m2 PO BD with Radiation therapy. After 6 weeks of completion of Chemoradiotherapy, advised six cycles of consolidative chemotherapy, CAPEOX regimen, Oxaliplatin 130mg/m2 on day 1 and Capecitabine 1000mg/m2 PO BD on days 1-14 repeated on a 21-day cycle for a total of six cycles. The primary endpoint is Disease-free survival (DFS); the secondary endpoint is adverse events related to chemoradiotherapy. Radiation toxicity is assessed by RTOG criteria, and chemotherapy toxicity is assessed by Common Terminology Criteria for Adverse Events (CTCAE) Version 5.0. Results: After 6 weeks of completion of Chemoradiotherapy, we did PET-CT of all three patients; all three patients had a clinically complete response and we advised 6 cycles of consolidative chemotherapy. After completion of consolidative chemotherapy, again PET-CT and sigmoidoscopy, all three patients had complete response on PET-CT and no lesions on sigmoidoscopy and kept all three patients on wait and watch.2 patients had Grade 2 skin toxicities,1 patient had Grade 1 skin toxicity, .2 patients had Grade 2 lower GI toxicities, and 1 patient had Grade lower GI toxicity, both according to RTOG criteria. 3 patients had Grade 2 diarrhea due to capecitabine, and 1 patient had Grade 1 thrombocytopenia due to oxaliplatin assessed by Common Terminology Criteria for Adverse Events (CTCAE) Version 5.0. Conclusion: Sphincter Preservation is possible with this regimen in those who don’t want to opt for surgery or in case of low-lying rectal cancer.

Keywords: locally advanced rectal cancer, sphincter preservation, chemoradiotherapy, consolidative chemotherapy

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Authors: María Fernanda Quiceno Vallejo, Patricia del Portillo, María Mercedes Zambrano, Jeisson Alejandro Triana, Dayana Calderon, Juan Manuel Anzola

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Microorganisms from tropical ecosystems can be novel in terms of adaptations and conservation. Given the macrodiversity of Colombian ecosystems, it is possible that this diversity is also present in Colombian soils. Tropical soil bacteria could offer a potentially novel source of bioactive compounds. In this study we analyzed a metagenomic fosmid library constructed with tropical bacterial DNAs with the aim of understanding its underlying diversity and functional potential. 8640 clones from the fosmid library were sequenced by NANOPORE MiniOn technology, then analyzed with bioinformatic tools such as Prokka, AntiSMASH and Bagel4 in order to identify functional biosynthetic pathways in the sequences. The strains showed ample difference when it comes to biosynthetic pathways. In total we identified 4 pathways related to aryl polyene synthesis, 12 related to terpenes, 22 related to NRPs (Non ribosomal peptides), 11 related PKs (Polyketide synthases) and 7 related to RiPPs (bacteriocins). We designed primers for the metagenomic clones with the most BGCs (sample 6 and sample 2). Results show the biotechnological / pharmacological potential of tropical ecosystems. Overall, this work provides an overview of the genomic and functional potential of Colombian soil and sets the groundwork for additional exploration of tropical metagenomic sequencing.

Keywords: bioactives, biosyntethic pathways, bioinformatic, bacterial gene clusters, secondary metabolites

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Authors: Shelley Harrington

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As a result of increasingly dynamic business environments, the creation and fostering of dynamic capabilities, [those capabilities that enable sustained competitive success despite of dynamism through the awareness and reconfiguration of internal and external competencies], supported by organisational learning [a dynamic capability] has gained increased and prevalent momentum in the research arena. Presenting findings funded by the Economic Social Research Council, this paper investigates the extent to which Senior Management Team (SMT) personality (at the trait and facet level) is associated with the creation of dynamic managerial capabilities at the team level, and effective organisational learning/knowledge sharing within the firm. In doing so, this research highlights the importance of micro-foundations in organisational psychology and specifically dynamic capabilities, a field which to date has largely ignored the importance of psychology in understanding these important and necessary capabilities. Using a direct measure of personality (NEO PI-3) at the trait and facet level across 32 high technology and finance firms in the UK, their CEOs (N=32) and their complete SMTs [N=212], a new measure of dynamic managerial capabilities at the team level was created and statistically validated for use within the work. A quantitative methodology was employed with regression and gap analysis being used to show the empirical foundations of personality being positioned as a micro-foundation of dynamic capabilities. The results of this study found that personality homogeneity within the SMT was required to strengthen the dynamic managerial capabilities of sensing, seizing and transforming, something which was required to reflect strong organisational learning at middle management level [N=533]. In particular, it was found that the greater the difference [t-score gaps] between the personality profiles of a Chief Executive Officer (CEO) and their complete, collective SMT, the lower the resulting self-reported nature of dynamic managerial capabilities. For example; the larger the difference between a CEOs level of dutifulness, a facet contributing to the definition of conscientiousness, and their SMT’s level of dutifulness, the lower the reported level of transforming, a capability fundamental to strategic change in a dynamic business environment. This in turn directly questions recent trends, particularly in upper echelons research highlighting the need for heterogeneity within teams. In doing so, it successfully positions personality as a micro-foundation of dynamic capabilities, thus contributing to recent discussions from within the strategic management field calling for the need to empirically explore dynamic capabilities at such a level.

Keywords: dynamic managerial capabilities, senior management teams, personality, dynamism

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Authors: Jianhua Zhang, Weiping Chen, Guanjie Chen, Jason Flannick, Emma Fikse, Glenda Smerin, Yanqin Yang, Yulong Li, John A. Hanover, William F. Simonds

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Ethnic disparities in many diseases are well recognized and reflect the consequences of genetic, behavior, and environmental factors. However, direct scientific evidence connecting the ethnic genetic variations and the disease disparities has been elusive, which may have led to the ethnic inequalities in large scale genetic studies. Through the genome-wide analysis of data representing 185,934 subjects, including 14,955 from our own studies of the African America Diabetes Mellitus, we discovered sets of genetic variants either unique to or conserved in all ethnicities. We further developed a quantitative gene function-based high-risk variant index (hrVI) of 20,428 genes to establish profiles that strongly correlate with the subjects' self-identified ethnicities. With respect to the ability to detect human essential and pathogenic genes, the hrVI analysis method is both comparable with and complementary to the well-known genetic analysis methods, pLI and VIRlof. Application of the ethnicity-specific hrVI analysis to the type 2 diabetes mellitus (T2DM) national repository, containing 20,791 cases and 24,440 controls, identified 114 candidate T2DM-associated genes, 8.8-fold greater than that of ethnicity-blind analysis. All the genes identified are defined as either pathogenic or likely-pathogenic in ClinVar database, with 33.3% diabetes-associated and 54.4% obesity-associated genes. These results demonstrate the utility of hrVI analysis and provide the first genetic evidence by clustering patterns of how genetic variations among ethnicities may impede the discovery of diabetes and foreseeably other disease-associated genes.

Keywords: diabetes-associated genes, ethnic health disparities, high-risk variant index, hrVI, T2DM

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Authors: Younis Elhaddad, Alfonso Ortega

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Oil production by means of gas lift is a standard technique in oil production industry. To optimize the total amount of oil production in terms of the amount of gas injected is a key question in this domain. Different methods have been tested to propose a general methodology. Many of them apply well-known numerical methods. Some of them have taken into account the power of evolutionary approaches. Our goal is to provide the experts of the domain with a powerful automatic searching engine into which they can introduce their knowledge in a format close to the one used in their domain, and get solutions comprehensible in the same terms, as well. These proposals introduced in the genetic engine the most expressive formal models to represent the solutions to the problem. These algorithms have proven to be as effective as other genetic systems but more flexible and comfortable for the researcher although they usually require huge search spaces to justify their use due to the computational resources involved in the formal models. The first step to evaluate the viability of applying our approaches to this realm is to fully understand the domain and to select an instance of the problem (gas lift optimization) in which applying genetic approaches could seem promising. After analyzing the state of the art of this topic, we have decided to choose a previous work from the literature that faces the problem by means of numerical methods. This contribution includes details enough to be reproduced and complete data to be carefully analyzed. We have designed a classical, simple genetic algorithm just to try to get the same results and to understand the problem in depth. We could easily incorporate the well mathematical model, and the well data used by the authors and easily translate their mathematical model, to be numerically optimized, into a proper fitness function. We have analyzed the 100 curves they use in their experiment, similar results were observed, in addition, our system has automatically inferred an optimum total amount of injected gas for the field compatible with the addition of the optimum gas injected in each well by them. We have identified several constraints that could be interesting to incorporate to the optimization process but that could be difficult to numerically express. It could be interesting to automatically propose other mathematical models to fit both, individual well curves and also the behaviour of the complete field. All these facts and conclusions justify continuing exploring the viability of applying the approaches more sophisticated previously proposed by our research group.

Keywords: evolutionary automatic programming, gas lift, genetic algorithms, oil production

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Authors: Szilvia Vincze, Zoltán Bács

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It has become increasingly important for institutions of higher education as well to use available resources as effectively as possible for the implementation of the institution’s strategic plans and, at the same time, to ensure a stable future. This is the responsibility of the management and administration of the institution. Having access to complete and comprehensive information is indispensable for making dynamic and well-founded decisions that consider the realization of objectives to be primary and that manage possibly emerging risks, etc. The present paper introduces the role of Management Information Systems (MIS) at the University of Debrecen, one of the largest institutions of higher education in Hungary, and also discusses the utilization of this and associated information systems in management functions.

Keywords: management information system (MIS), higher education, Hungary, strategy formulation

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Authors: J. T. Manhire

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A tax authority wants to take actions it knows will foster the greatest degree of voluntary taxpayer compliance to reduce the “tax gap.” This paper suggests that even if a tax authority could attain a state of complete knowledge, there are constraints on whether and to what extent such actions would result in reducing the macro-level tax gap. These limits are not merely a consequence of finite agency resources. They are inherent in the system itself. To show that this is one possible interpretation of the tax gap data, the paper formulates known results in a different way by analyzing tax compliance as a population with a single covariate. This leads to a standard use of the logistic map to analyze the dynamics of non-compliance growth or decay over a sequence of periods. This formulation gives the same results as the tax gap studies performed over the past fifty years in the U.S. given the published margins of error. Limitations and recommendations for future work are discussed, along with some implications for tax policy.

Keywords: income tax, logistic map, tax compliance, tax law

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Authors: Yamunah Devi Apalasamy, Sanjay Rampal, Tin Tin Su, Foong Ming Moy, Hazreen Abdul Majid, Awang Bulgiba, Zahurin Mohamed

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Obesity is a growing global health issue. Obesity results from a combination of environmental and genetics factors. Brain-derived neurotrophic factor (BDNF), a gene encodes the BDNF protein and the BDNF gene have been linked to regulation of body weight and appetite. Genome-wide association studies have identified the BDNF variants to be related to obesity among Caucasians, East Asians, and Filipinos. However, the role of BDNF in other ethnic groups remains inconclusive. This case control study aims to investigate the associations of BDNF gene polymorphisms with obesity and metabolic parameters in Malaysian Malays. BDNF rs4074134, BDNF rs10501087 and BDNF rs6265 were genotyped using Sequenom MassARRAY. Anthropometric, body fat, fasting lipids and glucose levels were measured. A total of 663 subjects (194 obese and 469 non-obese) were included in this study. There were no significant associations association between BDNF SNPs and obesity. The allelic and genotype frequencies of the BDNF SNPs were similar in the obese and non-obese groups. After adjustment for age and sex, the BDNF variants were not associated with obesity, body fat, fasting lipids and glucose levels. Haplotypes at the BDNF gene region, were not significantly associated with obesity. The BDNF rs4074134 was in strong LD with BDNF rs10501087 (D'=0.98) and BDNF rs6265 (D'=0.87). The BDNF rs10501087 was also in strong LD with BDNF rs6265 (D'=0.91). Our findings suggest that the BDNF variants and the haplotypes of BDNF gene were not associated with obesity and metabolic traits in this study population. Further research is needed to explore other BDNF variants with a larger sample size with gene-environment interactions in multi ethnic Malaysian population.

Keywords: genomics of obesity, SNP, BMI, haplotypes

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Authors: Md Habibul Ansary, Chandan Garai, Ranjan Dasgupta

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Utilization of resources is always a great challenge for any allocation problem, particularly when resource availability is dynamic in nature. In this work VM allocation mechanism has been augmented by providing resources in a combined manner. This approach has some inherent advantages in terms of reduction of wait state for the pending jobs of some users and better utilization of unused resources from the service providers’ point of view. Moreover the algorithm takes care of released resources from the finished jobs as soon as those become available. The proposed algorithm has been explained by suitable example to make the work complete.

Keywords: Bid ratio, cloud service, virtualization, VM allocation problem

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Authors: Zainul A. Khan, Malik Z. Abdin, Jawaid A. Khan

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Begomoviruses belonging to the family Geminiviridae, have single-stranded circular DNA genomes that are monopartite or bipartite. The large intergenic region (LIR) of the monopartite and common region (CR) of bipartite begomoviruses possess promoter activity in their genomes. In this study, we have characterized novel bidirectional promoters from Cotton leaf curl Burewala virus (CLCuBuV) genome using high-throughput software and analyzed with PlantCARE, PLACE, Cister and PlantPAN databases. The promoters (Rep and CP promoters) were assayed both in stable and transient expression systems in tobacco as well as cotton plants. Rep and CP-based promoters from the LIR sequence of CLCuBuV and 35S promoter of Cauliflower mosaic virus (CaMV) were tagged with β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes to check the efficacy of the promoters. Histochemical staining of GUS in transformed tobacco (Nicotiana tabacum cv. Xanthi) leaves showed higher GUS expression driven by CLCuBuV Rep (complimentary sense) promoter as compared to conventional CaMV 35S promoter and CLCuBuV CP (virion sense) promoter, respectively. GUS activity in individual plant cells driven by CLCuBuV Rep, CLCuBuV CP, and CaMV 35S promoter were quantified through fluorometric GUS assay and reverse transcription quantitative real-time PCR (RT-qPCR). The expression level of GUS tagged with CLCuBuV Rep promoter in the transformed tobacco plants was obtained 2 to 4 fold higher than CaMV 35S promoter. When CLCuBuV CP promoter was used, lower expression level was monitored than that by CaMV 35S promoter. The expression of GFP-tagged with CLCuBuV promoters was also investigated through agroinfiltration. The CLCuBuV Rep promoters showed stronger consistent transient expression in the leaves of N. benthamiana, N. tabacum and Gossypium hirsutum plants when compared with CaMV 35S and CLCuBuV CP promoter.

Keywords: Begmovirus, bidirectional promoter, CaMV 35S promoter, GFP, GUS, qPCR

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Authors: G. R. Hashemi Tabar, G. R. Razmi, F. Mirshekar

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Echinococcus granulosus have ten strains from G1 to G9. Each strain is related to special intermediated host. The morphology, epidemiology, treatment and control in these strains are different. There are many morphological and molecular methods to differentiate of Echinococcus strains. However, using both methods were provided better information about identification of each strain. The aim of study was to identify Echinococcus granulosus strain of hydrated cysts in slaughtered sheep using morphological and molecular methods in Mashhad area. In the present study, the infected liver and lung with hydatid cysts were collected and transferred to laboratory. The hydatid cyst liquid was extracted and morphological characters of rostellar hook protosclocies were measured using micrometer ocular. The total length of large blade length of large hooks, total length of small and blade length of small hooks, and number of hooks per protoscolex were 23± 0.3μm, 11.7±0.5 μm, 19.3±1.1 μm,8±1.1 and 33.7±0.7 μm, respectively. In molecular section of the study, DNA each samples was extracted with MBST Kit and development of PCR using special primers (EgF, EgR) which amplify fragment of ITS1 gen. The PCR product was digested with Bsh1236I enzyme. Based on pattern of PCR-RLFP results (four band forming), G1, G2 and G3 strain of Echinococcus granulosus were obtained. Differentiation of three strains was done using sequencing analysis and G1 strain was diagnosed. The agreement between the molecular results with morphometric characters of rosetellar hook was confirmed the presence of G1 strain of Echinococcus in the slaughtered sheep of Mashhad area.

Keywords: Echinococcus granulosus, Hydatid cyst, PCR, sheep

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Authors: Samina Jam Nazeer Ahmad, Samia Yasin, Ijaz Ahmad, Muhammad Tahir, Jam Nazeer Ahmad

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Phytoplasmas are phloem-inhibited plant pathogenic bacteria that are transferred by insect vectors. Among biotic factors, Phytoplasma infection induces abnormality influencing the physiology as well as morphology of plants. In 16Sr-IX group phytoplasma-infected brassica compestris, flower abnormalities have been associated with changes in the expression of floral development genes. To determine whether methylation was involved in down-regulation of flower development, the process of DNA methylation and Demethylation was investigated as a possible mechanism for regulation of floral gene expression in phytoplasma infected Brassica transmitted by Orosious orientalis vector by using RT-PCR, MSRE-PCR, Southern blotting, Bisulfite Sequencing, etc. Transcriptional expression of methylated genes was found to be globally down-regulated in plants infected with phytoplasma, but not severely in those infested by insect vectors and variation in expression was found in genes involved in methylation. These results also showed that genes particularly orthologous to Arabidopsis APETALA3 involved in petal formation and flower development was down-regulated severely in phytoplasma-infected brassica and with the fact that phytoplasma and insect induce variation in developmental gene expression. The DNA methylation status of flower developmental gene in phytoplasma infected plants with 5-azacytidine restored gene expression strongly suggesting that DNA methylation was involved in down-regulation of floral development genes in phytoplasma infected brassica.

Keywords: genes expression, phytoplasma, DNA methylation, flower development

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Authors: Chris George, Adam Hamlin, Lily Pereg, Richard Charlesworth, Gal Winter

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Background: According to the ‘hygiene hypothesis’ the current rise in allergies and autoimmune diseases stems mainly from reduced microbial exposure due, amongst other factors, to urbanisation and distance from soil. However, this hypothesis is based on epidemiological and not biological data. Useful insights into the underlying mechanisms of this hypothesis can be gained by studying our interaction with soil. Soil microbiota may be directly ingested or inhaled by humans, enter the body through skin-soil contact or using plants as vectors. This study aims to examine the ability of soil microbiota to colonise the gut, study the interaction of soil microbes with the immune system and their potential protective activity. Method: The nutrition of the rats was supplemented daily with fresh or autoclaved soil for 21 days followed by 14 days of no supplementations. Faecal samples were collected throughout and analysed using 16S sequencing. At the end of the experiment rats were sacrificed and tissues and digesta were collected. Results/Conclusion: Results showed significantly higher richness and diversity following soil supplementation even after recovery. Specific soil microbial groups identified as able to colonise the gut. Of particular interest was the mucosal layer which emerged as a receptive host for soil microorganisms. Histological examination revealed innate and adaptive immune activation. Findings of this study reinforce the ‘hygiene hypothesis’ by demonstrating the ability of soil microbes to colonise the gut and activate the immune system. This paves the way for further studies aimed to examine the interaction of soil microorganisms with the immune system.

Keywords: gut microbiota, hygiene hypothesis, microbiome, soil

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Authors: Rebecca-Lee Kuhnert, Ron Rapee

Abstract:

Up to 15% of Australian youth will experience an emotional disorder, yet relatively few get the help they need. Schools provide an ideal environment through which we can identify young people who are struggling and provide them with appropriate help. Universal mental health screening is a method by which all young people in school can be quickly assessed for emotional disorders, after which identified youth can be linked to appropriate health services. Despite the obvious logic of this process, universal mental health screening has received little scientific evaluation and even less application in Australian schools. This study will develop methods for Australian education systems to help identify young people (aged 9-17 years old) who are struggling with existing and emerging emotional disorders. Prior to testing, a series of focus groups will be run to get feedback and input from young people, parents, teachers, and mental health professionals. They will be asked about their thoughts on school-based screening methods and and how to best help students at risk of emotional distress. Schools (n=91) across New South Wales, Australia will be randomised to do either immediate screening (in May 2021) or delayed screening (in February 2022). Students in immediate screening schools will complete a long online mental health screener consisting of standard emotional health questionnaires. Ultimately, this large set of items will be reduced to a small number of items to form the final brief screener. Students who score in the “at-risk” range on any measure of emotional health problems will be identified to schools and offered pathways to relevant help according to the most accepted and approved processes identified by the focus groups. Nine months later, the same process will occur among delayed screening schools. At this same time, students in the immediate screening schools will complete screening for a second time. This will allow a direct comparison of the emotional health and help-seeking between youth whose schools had engaged in the screening and pathways to care process (immediate) and those whose schools had not engaged in the process (delayed). It is hypothesised that there will be a significant increase in students who receive help from mental health support services after screening, compared with baseline. It is also predicted that all students will show significantly less emotional distress after screening and access to pathways of care. This study will be an important contribution to Australian youth mental health prevention and early intervention by determining whether school screening leads to a greater number of young people with emotional disorders getting the help that they need and improving their mental health outcomes.

Keywords: children and young people, early intervention, mental health, mental health screening, prevention, school-based mental health

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Authors: Michael Adebayo, Saheed Lawal

Abstract:

The Comprehensive Geriatric Assessment (CGA) is the multidimensional tool used to assess elderly, frail patients either on admission to hospital care or at a community level in primary care. It is a tool designed with the aim of using a holistic approach to managing patients. A Cochrane review of CGA use in 2011 found that the likelihood of being alive and living in their own home rises by 30% post-discharge. RCTs have also discovered 10–15% reductions in readmission rates and reductions in institutionalization, and resource use and costs. Past audit cycles at King’s College Hospital, Denmark Hill had shown inconsistent evidence of CGA completion inpatient discharge summaries (less than 50%). Junior Doctors in the Health and Ageing (HAU) wards have struggled to sustain the efforts of past audit cycles due to the quick turnover in staff (four-month placements for trainees). This 7th cycle created a multi-faceted approach to solving this problem amongst staff and creating lasting change. Methods: 1. We adopted multidisciplinary team involvement to support Doctors. MDT staff e.g. Nurses, Physiotherapists, Occupational Therapists and Dieticians, were actively encouraged to fill in the CGA document. 2. We added a CGA Document Pro-forma to “Sunrise EPR” (Trust computer system). These CGAs were to automatically be included the discharge summary. 3. Prior to assessing uptake, we used a spot audit questionnaire to assess staff awareness/knowledge of what a CGA was. 4. We designed and placed posters highlighting domains of CGA and MDT roles suited to each domain on geriatric “Health and Ageing Wards” (HAU) in the hospital. 5. We performed an audit of % discharge summaries which include CGA and MDT role input. 6. We nominated ward champions on each ward from each multidisciplinary specialty to monitor and encourage colleagues to actively complete CGAs. 7. We initiated further education of ward staff on CGA's importance by discussion at board rounds and weekly multidisciplinary meetings. Outcomes: 1. The majority of respondents to our spot audit were aware of what a CGA was, but fewer had used the EPR document to complete one. 2. We found that CGAs were not being commenced for nearly 50% of patients discharged on HAU wards and the Frailty Assessment Unit.

Keywords: comprehensive geriatric assessment, CGA, multidisciplinary team, quality of life, mortality

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Authors: Sarada Nivedita Bhuyan

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Earthquake is the sudden, rapid movement of the earth’s crust and is the natural means of releasing stress. Tectonic plates play a major role for earthquakes as tectonic plates are the crust of the planet. The boundary lines of tectonic plates are usually known as fault lines. To understand an earthquake before its occurrence, different types of earthquake precursors are studied by different researchers. Surface temperature, strange cloud cover, earth’s electric field, geomagnetic phenomena, ground water level, active faults, ionospheric anomalies, tectonic movements are taken as parameters for earthquake study by different researchers. In this paper we tried to gather complete and helpful information of earthquake precursors which have been studied until now.

Keywords: earthquake precursors, earthquake, tectonic plates, fault

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Authors: Arab M., Ait Abdallah M., Zeraoulia N., Boumaza H., Aoutia M., Griene L., Ait Abdelkader B.,

Abstract:

breast and ovarian cancer are respectively the first and fourth leading causes of cancer among women in Algeria. A family story of cancer in the most important risk factor, and in most cases of families with breast and /or ovarian cancer, the pattern of cancer family can be attributed to mutation in BRCA1/2genes. objectibes: the aim of our study in to investigate the spectrum of BRCA1/2 germiline mutation in familial breast and /or ovarian cancer and to determine the prevalence and the nature of BRCA1/2mutation in Algeria methods: we deremined the prevalence of BRCA1/2 mutation within a cohort of 161 probands selected according the eisinger score double stranded sanger sequencing of all coding exons of BRCA1/2including flanking intronic region were performed results: we identified a total of 23 distinct deleterious mutations (class5) 12 differents mutations in BRCA1(52%) and 11 in BRCA2(48%). 78% (18/23) were protein truncating and 22%(5/23) missens mutations.3 novel deleterious mutations have been identified, which have not been described in public mutation database. one new mutation were found in two unrelated patients. the overall mutation detection rate in our study is 28,5%(46/161).more over, an UVS c7783 located in BRCA2 is found in two unrelated probands and segregate in the 02 families/ conclusion: our results sugget of large spectrum of BRCA1/2 mutation in Algerian breast/ovarian cancer family. The nature and prevalence of BRCA1/2mutation in algerian families are ongoing in a larger study, 80 probands are to day under investigation. This study which may therefore identify the genetic particularity of Algerian breast /ovarian cancer.

Keywords: BRCA1/2 mutations, hereditary breast cancer, algerian women, prvalence

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Authors: Abu Salim Mustafa

Abstract:

Rv3873 is a relatively large size protein (371 amino acids in length) and its gene is located in the immunodominant genomic region of difference (RD)1 that is present in the genome of Mycobacterium tuberculosis but deleted from the genomes of all the vaccine strains of Bacillus Calmette Guerin (BCG) and most other mycobacteria. However, when tested for cellular immune responses using peripheral blood mononuclear cells from tuberculosis patients and BCG-vaccinated healthy subjects, this protein was found to be a major stimulator of cell mediated immune responses in both groups of subjects. In order to further identify the sequence of immunodominant epitopes and explore their Human Leukocyte Antigen (HLA)-restriction for epitope recognition, 24 peptides (25-mers overlapping with the neighboring peptides by 10 residues) covering the sequence of Rv3873 were synthesized chemically using fluorenylmethyloxycarbonyl chemistry and tested in cell mediated immune responses. The results of these experiments helped in the identification of an immunodominant peptide P9 that was recognized by people expressing varying HLA-DR types. Furthermore, it was also predicted to be a promiscuous binder with multiple epitopes for binding to HLA-DR, HLA-DP and HLA-DQ alleles of HLA-class II molecules that present antigens to T helper cells, and to HLA-class I molecules that present antigens to T cytotoxic cells. In addition, the evaluation of peptide P9 using an immunogenicity predictor server yielded a high score (0.94), which indicated a greater probability of this peptide to elicit a protective cellular immune response. In conclusion, P9, a peptide with multiple epitopes and ability to bind several HLA class I and class II molecules for presentation to cells of the cellular immune response, may be useful as a peptide-based vaccine against tuberculosis.

Keywords: mycobacterium tuberculosis, PPE68, peptides, vaccine

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Authors: Elsheikh Asser

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Time and cost are the main goals of the construction project management. The first schedule developed may not be a suitable schedule for beginning or completing the project to achieve the target completion time at a minimum total cost. In general, there are trade-offs between time and cost (TCT) to complete the activities of a project. This research presents genetic algorithms (GAs) multi-objective model for project scheduling considering different scenarios such as least cost, least time, and target time.

Keywords: genetic algorithms, time-cost trade-off, multi-objective model, project scheduling

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Authors: Yeon Ho Je

Abstract:

A novel recombinant baculovirus, NeuroBactrus, was constructed to develop an improved baculovirus insecticide with additional beneficial properties, such as a higher insecticidal activity and improved recovery, compared to wild-type baculovirus. For the construction of NeuroBactrus, the Bacillus thuringiensis crystal protein gene (here termed cry1-5) was introduced into the Autographa californica nucleopolyhedrovirus (AcMNPV) genome by fusion of the polyhedrin–cry1-5–polyhedrin genes under the control of the polyhedrin promoter. In the opposite direction, an insect-specific neurotoxin gene, AaIT, from Androctonus australis was introduced under the control of an early promoter from Cotesia plutellae bracovirus by fusion of a partial fragment of orf603. The polyhedrin–Cry1-5–polyhedrin fusion protein expressed by the NeuroBactrus was not only occluded into the polyhedra, but it was also activated by treatment with trypsin, resulting in an_65-kDa active toxin. In addition, quantitative PCR revealed that the neurotoxin was expressed from the early phase of infection. NeuroBactrus showed a high level of insecticidal activity against Plutella xylostella larvae and a significant reduction in the median lethal time against Spodoptera exigua larvae compared to those of wild-type AcMNPV. Rerecombinant mutants derived from NeuroBactrus in which AaIT and/or cry1-5 were deleted were generated by serial passages in vitro. Expression of the foreign proteins (B. thuringiensis toxin and AaIT) was continuously reduced during the serial passage of the NeuroBactrus. Moreover, polyhedra collected from S. exigua larvae infected with the serially passaged NeuroBactrus showed insecticidal activity similar to that of wild-type AcMNPV. These results suggested that NeuroBactrus could be recovered to wild-type AcMNPV through serial passaging.

Keywords: baculovirus, insecticide, neurotoxin, neurobactrus

Procedia PDF Downloads 307